Christian Brueffer
@brueffer.io
Consultant in #bioinformatics and #cancer applications @insilico.consulting (all things #genomics, #liquidbiopsy, and #workflows) • 🇸🇪 🇩🇪 • 🧬🖥️ • https://brueffer.io
ORCiD: 0000-0002-3826-0989
ORCiD: 0000-0002-3826-0989
Reposted by Christian Brueffer
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
November 10, 2025 at 9:32 AM
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Reposted by Christian Brueffer
Conda in the Packaging Spectrum: From pip to Docker to Nix
If conda is a distribution, where does it fit alongside pip, Docker, and Nix? Part 2 of the 3-part series! 🚀
#conda #packaging #python
conda.org/blog/conda-p...
If conda is a distribution, where does it fit alongside pip, Docker, and Nix? Part 2 of the 3-part series! 🚀
#conda #packaging #python
conda.org/blog/conda-p...
Conda in the Packaging Spectrum: From pip to Docker to Nix | conda.org
Part 2 of the 'Conda Is Not PyPI' series, placing conda among pip, Docker, and Nix and explaining its middle-path design.
conda.org
November 4, 2025 at 2:38 PM
Conda in the Packaging Spectrum: From pip to Docker to Nix
If conda is a distribution, where does it fit alongside pip, Docker, and Nix? Part 2 of the 3-part series! 🚀
#conda #packaging #python
conda.org/blog/conda-p...
If conda is a distribution, where does it fit alongside pip, Docker, and Nix? Part 2 of the 3-part series! 🚀
#conda #packaging #python
conda.org/blog/conda-p...
Reposted by Christian Brueffer
The Cluster of Excellence @greenrobust.de is hiring:
- Computer Scientist/Research data manager: shorturl.at/xSvvO
- Data steward: shorturl.at/l6NCv
- Scientific coordinator 'Plant Perturbation Atlas': shorturl.at/vBU6x
Deadline: Friday, 7 November 2025
RT are welcome
#plantjobs #plantscijobs
- Computer Scientist/Research data manager: shorturl.at/xSvvO
- Data steward: shorturl.at/l6NCv
- Scientific coordinator 'Plant Perturbation Atlas': shorturl.at/vBU6x
Deadline: Friday, 7 November 2025
RT are welcome
#plantjobs #plantscijobs
Stellenangebote: Universität Hohenheim
Aktuelle Stellenangebote der Universität Hohenheim.
www.uni-hohenheim.de
October 7, 2025 at 9:59 AM
The Cluster of Excellence @greenrobust.de is hiring:
- Computer Scientist/Research data manager: shorturl.at/xSvvO
- Data steward: shorturl.at/l6NCv
- Scientific coordinator 'Plant Perturbation Atlas': shorturl.at/vBU6x
Deadline: Friday, 7 November 2025
RT are welcome
#plantjobs #plantscijobs
- Computer Scientist/Research data manager: shorturl.at/xSvvO
- Data steward: shorturl.at/l6NCv
- Scientific coordinator 'Plant Perturbation Atlas': shorturl.at/vBU6x
Deadline: Friday, 7 November 2025
RT are welcome
#plantjobs #plantscijobs
Reposted by Christian Brueffer
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Christian Brueffer
A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing.
www.uu.se/en/about-uu/...
www.uu.se/en/about-uu/...
Postdoctoral position - Uppsala University
Postdoctoral position, Department of Immunology, Genetics and Pathology, Uppsala University
www.uu.se
August 19, 2025 at 1:21 PM
A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing.
www.uu.se/en/about-uu/...
www.uu.se/en/about-uu/...
Reposted by Christian Brueffer
📣📣 Cool job alert! The @bakerresearchau.bsky.social is recruiting up to 2 new PIs in Biomedical Data Science 👉 www.seek.com.au/job/85989791...
You’d join an awesome institute in an incredible city (Melbourne, Australia) as well as partnerships like with @cam.ac.uk… you’ll also get to work with me 😁
You’d join an awesome institute in an incredible city (Melbourne, Australia) as well as partnerships like with @cam.ac.uk… you’ll also get to work with me 😁
July 25, 2025 at 7:24 AM
📣📣 Cool job alert! The @bakerresearchau.bsky.social is recruiting up to 2 new PIs in Biomedical Data Science 👉 www.seek.com.au/job/85989791...
You’d join an awesome institute in an incredible city (Melbourne, Australia) as well as partnerships like with @cam.ac.uk… you’ll also get to work with me 😁
You’d join an awesome institute in an incredible city (Melbourne, Australia) as well as partnerships like with @cam.ac.uk… you’ll also get to work with me 😁
Reposted by Christian Brueffer
📣 🥳 🧑💻 Our department is hiring:
Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark
Deadline June 1st
Thanks for sharing!
mbg.au.dk/en/news-and-...
Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark
Deadline June 1st
Thanks for sharing!
mbg.au.dk/en/news-and-...
Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark - Vacancy at Aarhus University
Vacancy at Department of Molecular Biology and Genetics - BiRC - Bioinformatics Research Center, Aarhus University
mbg.au.dk
May 16, 2025 at 12:35 PM
📣 🥳 🧑💻 Our department is hiring:
Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark
Deadline June 1st
Thanks for sharing!
mbg.au.dk/en/news-and-...
Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark
Deadline June 1st
Thanks for sharing!
mbg.au.dk/en/news-and-...
Reposted by Christian Brueffer
Minimap2-2.29 released with the support of short RNA-seq read alignment. More explanation and results here: lh3.github.io/2025/04/18/s...
Short RNA-seq read alignment with minimap2
lh3.github.io
April 18, 2025 at 9:53 PM
Minimap2-2.29 released with the support of short RNA-seq read alignment. More explanation and results here: lh3.github.io/2025/04/18/s...
Reposted by Christian Brueffer
🚀 Truvari v5.0 is here! 🎉
What’s new?
🔹 Enhanced symbolic variant support for, ,
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
What’s new?
🔹 Enhanced symbolic variant support for
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
GitHub - ACEnglish/truvari: Structural variant toolkit for VCFs
Structural variant toolkit for VCFs. Contribute to ACEnglish/truvari development by creating an account on GitHub.
github.com
January 10, 2025 at 1:43 PM
🚀 Truvari v5.0 is here! 🎉
What’s new?
🔹 Enhanced symbolic variant support for, ,
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
What’s new?
🔹 Enhanced symbolic variant support for
🔹 Robust BND comparison for cross-representation SV matching
🔹 Improved SV sequence similarity & HUGE SV support
🔹 Cleaner UI & Revamped API
👉 More: github.com/ACEnglish/tr...
#Genomics #Bioinformatics
Reposted by Christian Brueffer
#ICYMI our deep dive into ALK1 biology, at the intersection between angiogenesis and immunology with clear implication for the targeting of immunomodulatory cues & cancer therapy!
Targeting the most immune-suppressive macrophage with ALK1 inhibitors in malignant breast cancer!
@kpietraslab.bsky.social & team @lund-university.bsky.social target the most immune-suppressive macrophage with ALK1 inhibitors in malignant breast cancer models!
buff.ly/FXssb1x
@kpietraslab.bsky.social & team @lund-university.bsky.social target the most immune-suppressive macrophage with ALK1 inhibitors in malignant breast cancer models!
buff.ly/FXssb1x
March 13, 2025 at 3:51 PM
#ICYMI our deep dive into ALK1 biology, at the intersection between angiogenesis and immunology with clear implication for the targeting of immunomodulatory cues & cancer therapy!
Reposted by Christian Brueffer
BRCA1 turned 30 🎉
To celebrate, Jos Jonkers and I explored three decades of BRCA1 research - what we’ve learned about its biology, its role in tumorigenesis and future directions to improve the life of BRCA1 mutation carriers.
Now out in Cancer Discovery ⬇️: aacrjournals.org/cancerdiscov...
To celebrate, Jos Jonkers and I explored three decades of BRCA1 research - what we’ve learned about its biology, its role in tumorigenesis and future directions to improve the life of BRCA1 mutation carriers.
Now out in Cancer Discovery ⬇️: aacrjournals.org/cancerdiscov...
Thirty Years of BRCA1: Mechanistic Insights and Their Impact on Mutation Carriers
Abstract. Thirty years ago, the cloning of the first breast cancer susceptibility gene, BRCA1, marked a milestone in our understanding of hereditary breast and ovarian cancers. This discovery initiate...
aacrjournals.org
March 3, 2025 at 9:26 AM
BRCA1 turned 30 🎉
To celebrate, Jos Jonkers and I explored three decades of BRCA1 research - what we’ve learned about its biology, its role in tumorigenesis and future directions to improve the life of BRCA1 mutation carriers.
Now out in Cancer Discovery ⬇️: aacrjournals.org/cancerdiscov...
To celebrate, Jos Jonkers and I explored three decades of BRCA1 research - what we’ve learned about its biology, its role in tumorigenesis and future directions to improve the life of BRCA1 mutation carriers.
Now out in Cancer Discovery ⬇️: aacrjournals.org/cancerdiscov...
Reposted by Christian Brueffer
Our first curated draft somatic structural variant benchmark for the new GIAB PDAC tumor cell line HG008-T is at ftp-trace.ncbi.nlm.nih.gov/ReferenceSam..., based on extensive short+long read sequencing data described in doi.org/10.1101/2024.... Feedback to improve future versions is very welcome!
Index of /ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar_DraftBenchmark_V0.1-20241219
ftp-trace.ncbi.nlm.nih.gov
December 20, 2024 at 6:04 PM
Our first curated draft somatic structural variant benchmark for the new GIAB PDAC tumor cell line HG008-T is at ftp-trace.ncbi.nlm.nih.gov/ReferenceSam..., based on extensive short+long read sequencing data described in doi.org/10.1101/2024.... Feedback to improve future versions is very welcome!
Reposted by Christian Brueffer
Regular abstracts from #SABCS24 are out!
3407 pages of new breast cancer discoveries.
Find them here: sabcs.org/Portals/0/Do...
3407 pages of new breast cancer discoveries.
Find them here: sabcs.org/Portals/0/Do...
sabcs.org
November 25, 2024 at 11:41 PM
Regular abstracts from #SABCS24 are out!
3407 pages of new breast cancer discoveries.
Find them here: sabcs.org/Portals/0/Do...
3407 pages of new breast cancer discoveries.
Find them here: sabcs.org/Portals/0/Do...
Reposted by Christian Brueffer
WOOT!
Just in time for #SABCS24 looks like @sabcs.bsky.social is officially on BlueSky!
cc: @maryamlustberg.bsky.social @drsgraff.bsky.social @stage4kelly.bsky.social @amjohnston.bsky.social @amybeumer.bsky.social @raalbany.bsky.social @hoperugo.bsky.social
Just in time for #SABCS24 looks like @sabcs.bsky.social is officially on BlueSky!
cc: @maryamlustberg.bsky.social @drsgraff.bsky.social @stage4kelly.bsky.social @amjohnston.bsky.social @amybeumer.bsky.social @raalbany.bsky.social @hoperugo.bsky.social
two women are standing next to each other and one of them is saying i 'm so glad that you are here
ALT: two women are standing next to each other and one of them is saying i 'm so glad that you are here
media.tenor.com
November 21, 2024 at 6:42 PM
WOOT!
Just in time for #SABCS24 looks like @sabcs.bsky.social is officially on BlueSky!
cc: @maryamlustberg.bsky.social @drsgraff.bsky.social @stage4kelly.bsky.social @amjohnston.bsky.social @amybeumer.bsky.social @raalbany.bsky.social @hoperugo.bsky.social
Just in time for #SABCS24 looks like @sabcs.bsky.social is officially on BlueSky!
cc: @maryamlustberg.bsky.social @drsgraff.bsky.social @stage4kelly.bsky.social @amjohnston.bsky.social @amybeumer.bsky.social @raalbany.bsky.social @hoperugo.bsky.social
Reposted by Christian Brueffer
Dear Colleagues,
For all of you in BlueSky, Greetings, We are Now Here!!
We invite you to Join & Follow OncoAlert at @oncoalert.bsky.social
Thank you for your support!
For all of you in BlueSky, Greetings, We are Now Here!!
We invite you to Join & Follow OncoAlert at @oncoalert.bsky.social
Thank you for your support!
November 16, 2024 at 1:31 PM
Dear Colleagues,
For all of you in BlueSky, Greetings, We are Now Here!!
We invite you to Join & Follow OncoAlert at @oncoalert.bsky.social
Thank you for your support!
For all of you in BlueSky, Greetings, We are Now Here!!
We invite you to Join & Follow OncoAlert at @oncoalert.bsky.social
Thank you for your support!
November 16, 2024 at 1:02 PM
Reposted by Christian Brueffer
in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods
go.bsky.app/GmS1cH
go.bsky.app/GmS1cH
single-cell computational methods
Join the conversation
go.bsky.app
November 15, 2024 at 11:11 AM
in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods
go.bsky.app/GmS1cH
go.bsky.app/GmS1cH
Reposted by Christian Brueffer
Inspired by the other amazing starter packs - here's one for cancer researchers!
I tried to make this broad - from immunology to genomics to cell biology and so much more..
This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺
Hope its useful!
go.bsky.app/FEoaJMc
I tried to make this broad - from immunology to genomics to cell biology and so much more..
This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺
Hope its useful!
go.bsky.app/FEoaJMc
November 14, 2024 at 9:44 PM
Inspired by the other amazing starter packs - here's one for cancer researchers!
I tried to make this broad - from immunology to genomics to cell biology and so much more..
This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺
Hope its useful!
go.bsky.app/FEoaJMc
I tried to make this broad - from immunology to genomics to cell biology and so much more..
This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺
Hope its useful!
go.bsky.app/FEoaJMc
I've created a Breast Cancer Starter Pack covering clinical oncology and research. Please share, and let me know in case you'd like to be added. #brca #breastcancer
go.bsky.app/6KXpPSy
go.bsky.app/6KXpPSy
November 15, 2024 at 7:51 AM
I've created a Breast Cancer Starter Pack covering clinical oncology and research. Please share, and let me know in case you'd like to be added. #brca #breastcancer
go.bsky.app/6KXpPSy
go.bsky.app/6KXpPSy
Reposted by Christian Brueffer
We are actively recruiting for two open Computational Biology positions in our NGS group - both covered by this listing
www.ginkgobioworks.com/job-listings...
www.ginkgobioworks.com/job-listings...
April 13, 2024 at 4:55 PM
We are actively recruiting for two open Computational Biology positions in our NGS group - both covered by this listing
www.ginkgobioworks.com/job-listings...
www.ginkgobioworks.com/job-listings...
Happy to have contributed a small part to this study. "Ultrahigh" #HER2 copy number by #dPCR or #RNAseq signals poor response to adjuvant #trastuzumab in breast cancer.
Our new publication online today on dPCR quantification of “#ultrahigh” #HER2 #ERBB2 copy number in early #breastcancer and association to poor response to #trastuzumab. Nice work by #pei_meng #heena_dilal @brueffer.io #sergii_gladchuk #anna_ehinger et al www.nature.com/articles/s41...
Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab - npj Breast Cancer
npj Breast Cancer - Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab
www.nature.com
February 20, 2024 at 9:00 AM
Happy to have contributed a small part to this study. "Ultrahigh" #HER2 copy number by #dPCR or #RNAseq signals poor response to adjuvant #trastuzumab in breast cancer.
Reposted by Christian Brueffer
Online Hackathon to improve the annotation of @galaxyproject.bsky.social resources for microbial data analysis (and beyond): galaxyproject.org/events/2024-...
📆 Date: March 11th - 15th
📍 Location: Online via Zoom & chat. 2 daily stand-ups
👥 Participation: Free. Open to anyone, anywhere
📆 Date: March 11th - 15th
📍 Location: Online via Zoom & chat. 2 daily stand-ups
👥 Participation: Free. Open to anyone, anywhere
Hackathon - Improving the annotation of Galaxy resources for microbial
This hackathon aims to improve the annotation of Galaxy resources for microbial data analysis and beyond
galaxyproject.org
February 19, 2024 at 9:53 AM
Online Hackathon to improve the annotation of @galaxyproject.bsky.social resources for microbial data analysis (and beyond): galaxyproject.org/events/2024-...
📆 Date: March 11th - 15th
📍 Location: Online via Zoom & chat. 2 daily stand-ups
👥 Participation: Free. Open to anyone, anywhere
📆 Date: March 11th - 15th
📍 Location: Online via Zoom & chat. 2 daily stand-ups
👥 Participation: Free. Open to anyone, anywhere
Reposted by Christian Brueffer
Still a week to apply for this postdoc position to work with us on deep learning models for regulatory genomics 👇🏼
Looking for a postdoc in my group at NCMM, Nordic EMBL Partnership, to enhance computational resources for regulatory genomics (JASPAR & UniBind) with deep learning.
Project in collaboration with @anshulkundaje.bsky.social & @wywywa.bsky.social
Apply by Feb. 8th
www.jobbnorge.no/en/available...
Project in collaboration with @anshulkundaje.bsky.social & @wywywa.bsky.social
Apply by Feb. 8th
www.jobbnorge.no/en/available...
January 31, 2024 at 7:34 AM
Still a week to apply for this postdoc position to work with us on deep learning models for regulatory genomics 👇🏼
Reposted by Christian Brueffer
We will have a job ad for Japanese ecologists coming soon - any tips on breaking into the Japanese cluster here (i know its pretty big)? Good feeds or anything I can pop up in? (Other than, obviously, posting in Japanese).
January 30, 2024 at 9:34 AM
We will have a job ad for Japanese ecologists coming soon - any tips on breaking into the Japanese cluster here (i know its pretty big)? Good feeds or anything I can pop up in? (Other than, obviously, posting in Japanese).
Reposted by Christian Brueffer
Interested in breaking all your bioinformatic pipelines? Look no farther:
https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot
https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot
January 17, 2024 at 4:18 PM
Interested in breaking all your bioinformatic pipelines? Look no farther:
https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot
https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot